Man pages for andrewparkermorgan/popcorn
File-Format Wrangler for Population-Based Genetic Data
| dot-fix_sex | Encode sex as integer |
| dot-prep.layout | draw the characteristic TreeMix tree with migration edges |
| dot-sort_indiv | Internal helper function for sorting rows in ADMIXTURE... |
| myldply | A 'dplyr'-friendly equivalent to the old 'plyr::ldply()' |
| pca_plink | Perform PCA using 'plink2' |
| pca_vcf | Perform PCA on a VCF file using 'akt pca' and consume result |
| plot_admixture | Make standard stacked-bars plot of ancestry proportions. |
| plot_admixture_labelled | Make stacked-bar plot of ancestry proportions, with... |
| plot_treemix | Plot population tree |
| read_beagle_ibd | Read BEAGLE-format IBD segments |
| read_bed | Read genomic intervals in BED format |
| read_coverage | Read output from my 'coverage.py' script |
| read_fam | Read a PLINK family (*.fam) file |
| read_het_plink | Read estimated inbreeding report from PLINK |
| read_homozyg_plink | Read ROH report from PLINK |
| read_loglik_files | Read log-likelihoods from ADMIXTURE runs |
| read_map | Read a PLINK marker map (*.bim) file |
| read_Q_matrix | Read ancestry proportions ('Q-matrix') from ADMIXTURE run |
| read_roh | Read 'bcftools roh' output (mode '-Or") |
| read_treemix | Read TreeMix output files |
| scale_combo | Combined shape and colour scale for uniquely identifying many... |
| scale_shape_repeater | Discrete scale of different point shapes that repeats |
| sort_by_cluster | Sort samples by admixture components using crude heuristics |
| theme_admixture | A ggplot theme for ADMIXTURE plots |
| theme_nice | Clean-looking ggplot2 theme, similar to 'theme_classic()' |
| theme_slanty_x | Make ggplot2 x-axis labels slanted |
| theme_treemix | Plotting theme for TreeMix population trees |
| tidy | Convert admixture proportions to tidy format. |
